Hi there, it does seem like a mine field doesn't it.
We have a before and after school nanny too.
She arrives at 7.30am at our house, and drops off at school for around 8.40am. She doesn't come back to our house after, but we count that as 1.5 hours because like you, I don't want to quibble over 15 minutes, and days DCs take longer to get into class than other days.
She then picks up at 3.10pm, and stays until approx 6.45 - 7.00pm. depending on when we get home. We count that as 4 hours, and if we get home early, she's free to go, and we still count it as 4 hours.
She does two or three extra sessions during the week, when the DCs aren't around, to tidy their rooms, do laundry etc - probably around 5 additional hours in total.
We do actually pay our nanny a weekly standard amount. We agreed this because a: she does a different set of hours during the hols, and b: we want a bit of give and take, and some times there are school clubs that mean DCs aren't picked up until 4.15pm etc. which is not the nanny's problem, and we woudn't want her out of pocket because of this.
Therefore, she gets the same pay every week, which over the course of the year would probably even out at around (eg) £10.50 - £11.00 per hour gross. The way we work it, our nanny probably does better out of the deal than if we paid absolutely hourly pay according to the hours worked, which I am happy about because it makes for a good relationship.
We don't even consider lunch hours - she's paid for the whole time she's with us, term time and holidays.
I think the agencies will tell you one thing - eg - it MUST be an hourly rate, but if you go on nannyjobs, childcare uk etc., and meet a nanny that you are happy to work with, then you can work out your own arrangement with your nanny.
I think as long are you're fair, and the flexibility and balance works out evenly, then you should be fine.
Good luck with going back to work x